Alignments for a candidate for hisD in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisD in Nitriliruptor alkaliphilus DSM 45188

Align Histidinol dehydrogenase; HDH; EC 1.1.1.23 (characterized)
to candidate WP_083442240.1 NITAL_RS18765 histidinol dehydrogenase

Query= SwissProt::P9WNW9
         (444 letters)



>NCBI__GCF_000969705.1:WP_083442240.1
          Length = 433

 Score =  351 bits (900), Expect = e-101
 Identities = 209/427 (48%), Positives = 266/427 (62%), Gaps = 17/427 (3%)

Query: 27  LPRGGADVEAVLPTVRPIVAAVAERGAEAALDFGASFDGVRPHA---IRVPDAALDAALA 83
           +PR   D+ A    V   +A V  RG  A  D  A FD     A   + VPD  LDAAL 
Sbjct: 1   MPRPRVDLAAAREGVDATLADVKARGDAALRDLTARFDATEFGADEPLVVPDEVLDAALL 60

Query: 84  GLDCDVCEALQVMVERTRAVHSGQRRTDVTTTLGPGATVTERWVPVERVGLYVPGGNAVY 143
            LD ++  A++   ++ R  H   +  D       GA +   + P+ER G+YVPGG AVY
Sbjct: 61  DLDPELRAAIERAADQVRWFHERAKPEDWEDERD-GARMGVWFRPIERAGVYVPGGKAVY 119

Query: 144 PSSVVMNVVPAQAAGVDSLVVASPP-----QAQWDGMPHPTILAAARLLGVDEVWAVGGA 198
           PS+V+M VVPAQ AGVD +V+ +PP       + DG P+ TILAAARLLGVD V  VGGA
Sbjct: 120 PSTVIMTVVPAQVAGVDQIVLCTPPTGTGPDGERDGWPNRTILAAARLLGVDRVVRVGGA 179

Query: 199 QAVALLAYGGTDTDGAALTPVDMITGPGNIYVTAAKR--LCRSRVGIDAEAGPTEIAILA 256
           QAVA +AYG TD+  A     D + GPGN+YV+ AK+  +    +G D  AGPTE+ I+A
Sbjct: 180 QAVAAMAYG-TDSVPAC----DKVVGPGNLYVSLAKQRLVAEGVIGTDGYAGPTEVVIVA 234

Query: 257 DHTADPVHVAADLISQAEHDELAASVLVTPSEDLADATDAELAGQLQTTVHRERVTAALT 316
           D TADP  VAADL++QAEHDELA ++L+T   DL    +A L  ++    HRERV AAL 
Sbjct: 235 DGTADPRVVAADLVAQAEHDELATAMLITHDADLVAPVEAALEVEVTRAHHRERVEAALA 294

Query: 317 GRQSAIVLVDDVDAAVLVVNAYAAEHLEIQTADAPQVASRIRSAGAIFVGPWSPVSLGDY 376
           G Q  + LVDD+D AV V  A+AAEHLE+QT DA  VA RIR AG  F+G  +PVSLGDY
Sbjct: 295 G-QGTVALVDDIDQAVQVAEAFAAEHLEVQTVDARAVAERIRYAGTTFIGGPTPVSLGDY 353

Query: 377 CAGSNHVLPTAGCARHSSGLSVQTFLRGIHVVEYTEAALKDVSGHVITLATAEDLPAHGE 436
            AG NH LPT+G AR + GL+  +FL  ++ VEY + AL+ ++  V TLA +EDLPAH  
Sbjct: 354 AAGPNHTLPTSGTARFAGGLTTSSFLVPVNFVEYDQVALEGLAASVRTLAASEDLPAHAR 413

Query: 437 AVRRRFE 443
           AV  R E
Sbjct: 414 AVDVRLE 420


Lambda     K      H
   0.317    0.132    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 492
Number of extensions: 20
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 444
Length of database: 433
Length adjustment: 32
Effective length of query: 412
Effective length of database: 401
Effective search space:   165212
Effective search space used:   165212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_083442240.1 NITAL_RS18765 (histidinol dehydrogenase)
to HMM TIGR00069 (hisD: histidinol dehydrogenase (EC 1.1.1.23))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00069.hmm
# target sequence database:        /tmp/gapView.27772.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00069  [M=393]
Accession:   TIGR00069
Description: hisD: histidinol dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-142  459.7   1.2   5.6e-142  459.5   1.2    1.0  1  lcl|NCBI__GCF_000969705.1:WP_083442240.1  NITAL_RS18765 histidinol dehydro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_083442240.1  NITAL_RS18765 histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.5   1.2  5.6e-142  5.6e-142       2     393 .]      16     418 ..      15     418 .. 0.96

  Alignments for each domain:
  == domain 1  score: 459.5 bits;  conditional E-value: 5.6e-142
                                 TIGR00069   2 keiiedvrkeGdeAlleytekfdkv...kleslrvseeeleealeavdeelkealelaaeniekfhekq 67 
                                                + ++dv+++Gd+Al+++t +fd +     e l v++e l++al  +d+el++a+e+aa++++ fhe+ 
  lcl|NCBI__GCF_000969705.1:WP_083442240.1  16 DATLADVKARGDAALRDLTARFDATefgADEPLVVPDEVLDAALLDLDPELRAAIERAADQVRWFHERA 84 
                                               56789******************997777789************************************* PP

                                 TIGR00069  68 lpesveveteegvllgqkvrplervglYvPgGkaaypStvlmtavpAkvAgvkeivvvtPp.......k 129
                                               +pe++e ++++g  +g  +rp+er+g+YvPgGka ypStv+mt+vpA+vAgv++iv++tPp       +
  lcl|NCBI__GCF_000969705.1:WP_083442240.1  85 KPEDWE-DERDGARMGVWFRPIERAGVYVPGGKAVYPSTVIMTVVPAQVAGVDQIVLCTPPtgtgpdgE 152
                                               ****96.5689*************************************************955433322 PP

                                 TIGR00069 130 kdgkvnpavlaaakllgvdevykvGGaqaiaalayGtetvpkvdkivGPGniyVtaAKklvf..gevgi 196
                                               +dg  n+++laaa+llgvd+v++vGGaqa+aa+ayGt++vp++dk+vGPGn yV  AK+ ++  g +g 
  lcl|NCBI__GCF_000969705.1:WP_083442240.1 153 RDGWPNRTILAAARLLGVDRVVRVGGAQAVAAMAYGTDSVPACDKVVGPGNLYVSLAKQRLVaeGVIGT 221
                                               47789*****************************************************98876779*** PP

                                 TIGR00069 197 dmiaGPsEvlviadesanpelvaaDllsqaEHdedaqailvttseelaekveeeveeqleelerkeiae 265
                                               d  aGP+Ev+++ad +a+p++vaaDl++qaEHde a+a+l+t++++l++ ve+++e ++++++++e +e
  lcl|NCBI__GCF_000969705.1:WP_083442240.1 222 DGYAGPTEVVIVADGTADPRVVAADLVAQAEHDELATAMLITHDADLVAPVEAALEVEVTRAHHRERVE 290
                                               ********************************************************************* PP

                                 TIGR00069 266 kslekngaiilvddleealelsneyApEHLelqtkdpeellkkiknaGsvflGeytpealgdyvaGpnh 334
                                               ++l+ +g++ lvdd+++a+++++++A+EHLe+qt d+++++++i+ aG+ f+G  tp++lgdy+aGpnh
  lcl|NCBI__GCF_000969705.1:WP_083442240.1 291 AALAGQGTVALVDDIDQAVQVAEAFAAEHLEVQTVDARAVAERIRYAGTTFIGGPTPVSLGDYAAGPNH 359
                                               ********************************************************************* PP

                                 TIGR00069 335 vLPTsgtArfasglsvedFlkrisvqelskealeelaeaveklaeaEgLeaHaeavevR 393
                                               +LPTsgtArfa+gl++++Fl  ++++e+++ ale la +v++la+ E+L aHa+av+vR
  lcl|NCBI__GCF_000969705.1:WP_083442240.1 360 TLPTSGTARFAGGLTTSSFLVPVNFVEYDQVALEGLAASVRTLAASEDLPAHARAVDVR 418
                                               *********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (433 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.40
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis